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          <td width="10%" class="headerCovTableHead">Found</td>
          <td width="10%" class="headerCovTableHead">Hit</td>
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          <td class="headerValue">cover.info</td>
          <td class="headerItem">Lines:</td>
          <td class="headerCovTableEntry">33</td>
          <td class="headerCovTableEntry">33</td>
          <td class="headerCovTableEntryHi">100.0 %</td>
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          <td class="headerItem">Date:</td>
          <td class="headerValue">2010-08-03</td>
          <td class="headerItem">Functions:</td>
          <td class="headerCovTableEntry">7</td>
          <td class="headerCovTableEntry">7</td>
          <td class="headerCovTableEntryHi">100.0 %</td>
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<a name="1"><span class="lineNum">       1 </span>                : /**</a>
<span class="lineNum">       2 </span>                :  * \file  antiviral.h
<span class="lineNum">       3 </span>                :  * \brief Definition of Antiviral class.
<span class="lineNum">       4 </span>                :  *
<span class="lineNum">       5 </span>                :  * ASO: Antiviral Sequence Optimizer
<span class="lineNum">       6 </span>                :  * &lt;http://aso.googlecode.com/&gt;
<span class="lineNum">       7 </span>                :  * Copyright (C) 2010 Velez Ezequiel, Peralta Andres, FuDePAN
<span class="lineNum">       8 </span>                :  *
<span class="lineNum">       9 </span>                :  * This file is part of the ASO project.
<span class="lineNum">      10 </span>                :  *
<span class="lineNum">      11 </span>                :  * Contents:       Header file for ASO providing class Antiviral.
<span class="lineNum">      12 </span>                :  *
<span class="lineNum">      13 </span>                :  * System:         ASO
<span class="lineNum">      14 </span>                :  * Language:       C++
<span class="lineNum">      15 </span>                :  *
<span class="lineNum">      16 </span>                :  * Author:         Velez Ezequiel, Peralta Andres
<span class="lineNum">      17 </span>                :  * E-Mail:
<span class="lineNum">      18 </span>                :  *
<span class="lineNum">      19 </span>                :  * ASO is free software: you can redistribute it and/or modify
<span class="lineNum">      20 </span>                :  * it under the terms of the GNU General Public License as published by
<span class="lineNum">      21 </span>                :  * the Free Software Foundation, either version 3 of the License, or
<span class="lineNum">      22 </span>                :  * (at your option) any later version.
<span class="lineNum">      23 </span>                :  *
<span class="lineNum">      24 </span>                :  * ASO is distributed in the hope that it will be useful,
<span class="lineNum">      25 </span>                :  * but WITHOUT ANY WARRANTY; without even the implied warranty of
<span class="lineNum">      26 </span>                :  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
<span class="lineNum">      27 </span>                :  * GNU General Public License for more details.
<span class="lineNum">      28 </span>                :  *
<span class="lineNum">      29 </span>                :  * You should have received a copy of the GNU General Public License
<span class="lineNum">      30 </span>                :  * along with ASO.  If not, see &lt;http://www.gnu.org/licenses/&gt;.
<span class="lineNum">      31 </span>                :  *
<span class="lineNum">      32 </span>                :  */
<span class="lineNum">      33 </span>                : 
<span class="lineNum">      34 </span>                : #ifndef ANTIVIRAL_IMP_H
<span class="lineNum">      35 </span>                : #define ANTIVIRAL_IMP_H
<span class="lineNum">      36 </span>                : 
<span class="lineNum">      37 </span>                : #include &lt;mili/mili.h&gt;
<span class="lineNum">      38 </span>                : #include &quot;antiviral.h&quot;
<span class="lineNum">      39 </span>                : #include &quot;distance_matrix.h&quot;
<span class="lineNum">      40 </span>                : 
<span class="lineNum">      41 </span>                : const float MAX_VAL = 3.0f;
<span class="lineNum">      42 </span>                : const float ZERO_DISTANCE = 0.0f;
<span class="lineNum">      43 </span>                : 
<span class="lineNum">      44 </span>                : /*! Clase del antiviral. */
<span class="lineNum">      45 </span>                : enum AvClass
<span class="lineNum">      46 </span>                : {
<span class="lineNum">      47 </span>                :     cPI, /*! Class Protease Inhibitor.         */
<span class="lineNum">      48 </span>                :     cNRTI, /*! Class Nucletotide Reverse Transcriptasa Inhibitor  */
<span class="lineNum">      49 </span>                :     cNNRTI, /*! Class Non Nucletotide Reverse Transcriptase Inhibitor */
<span class="lineNum">      50 </span>                :     cComb    /*! Combinated class.           */
<span class="lineNum">      51 </span>                : };
<span class="lineNum">      52 </span>                : 
<span class="lineNum">      53 </span>                : /*! Tipo del Antiviral. */
<span class="lineNum">      54 </span>                : enum AvType
<span class="lineNum">      55 </span>                : {
<span class="lineNum">      56 </span>                :     tRT, /*! Type Reverse Transcriptasa. */
<span class="lineNum">      57 </span>                :     tPI, /*! Type Proteasa Inhibitor  */
<span class="lineNum">      58 </span>                :     tComb /*! Combinated Type    */
<span class="lineNum">      59 </span>                : };
<span class="lineNum">      60 </span>                : 
<span class="lineNum">      61 </span>                : /*! Para que funcióne bien el filter con enumerados*/
<span class="lineNum">      62 </span>                : std::ostream&amp; operator&lt;&lt; (std::ostream &amp;out, const AvType&amp; atype);
<span class="lineNum">      63 </span>                : std::ostream&amp; operator&lt;&lt; (std::ostream &amp;out, const AvClass&amp; aclass);
<span class="lineNum">      64 </span>                : std::istream&amp; operator&gt;&gt; (std::istream&amp; is, AvClass&amp; aclass);
<span class="lineNum">      65 </span>                : std::istream&amp; operator&gt;&gt; (std::istream&amp; is, AvType&amp; atype);
<span class="lineNum">      66 </span>                : 
<span class="lineNum">      67 </span>                : /*! Clase Antiviral:
<span class="lineNum">      68 </span>                :  Clase que implementa a un antiviral asociandoles una secuencia de aminoacidos, un nombre, un tipo,
<span class="lineNum">      69 </span>                :  una clase y un id unico.
<a name="70"><span class="lineNum">      70 </span>                : */</a>
<span class="lineNum">      71 </span>                : class ResisBasedAntiviral: public Antiviral
<span class="lineNum">      72 </span><span class="lineCov">             78 : {</span>
<span class="lineNum">      73 </span>                : public:
<span class="lineNum">      74 </span>                :     /* Posición de las Resistencias*/
<span class="lineNum">      75 </span>                :     struct ResistancePosition
<span class="lineNum">      76 </span>                :     {
<span class="lineNum">      77 </span>                :         size_t pos;
<a name="78"><span class="lineNum">      78 </span>                :         string  aminoacids;</a>
<span class="lineNum">      79 </span>                : 
<span class="lineNum">      80 </span><span class="lineCov">            534 :         ResistancePosition(size_t pos, const std::string aminoacids)</span>
<span class="lineNum">      81 </span><span class="lineCov">            534 :                 : pos(pos), aminoacids(aminoacids)</span>
<a name="82"><span class="lineNum">      82 </span><span class="lineCov">            534 :         {}</span></a>
<span class="lineNum">      83 </span>                : 
<span class="lineNum">      84 </span><span class="lineCov">            776 :         ResistancePosition(const ResistancePosition&amp; other)</span>
<span class="lineNum">      85 </span><span class="lineCov">            776 :                 : pos(other.pos), aminoacids(other.aminoacids)</span>
<a name="86"><span class="lineNum">      86 </span><span class="lineCov">            776 :         {}</span></a>
<span class="lineNum">      87 </span>                : 
<span class="lineNum">      88 </span><span class="lineCov">           1189 :         ~ResistancePosition() {}</span>
<a name="89"><span class="lineNum">      89 </span>                : </a>
<span class="lineNum">      90 </span>                :         //Retorna un par con la lista de tripletes y la distancia mínima.
<span class="lineNum">      91 </span><span class="lineCov">          38820 :         TripletVal min_dist_to_resistance(const NucSequence&amp; sequence) const</span>
<span class="lineNum">      92 </span>                :         {
<span class="lineNum">      93 </span><span class="lineCov">          38820 :             float min_dist(MAX_VAL);</span>
<span class="lineNum">      94 </span><span class="lineCov">          38820 :             TripletVal tval, min_list;</span>
<span class="lineNum">      95 </span><span class="lineCov">          38820 :             TripletList tlist;</span>
<span class="lineNum">      96 </span><span class="lineCov">          38820 :             const Triplet pos_triplet = sequence.get_triplet(pos);</span>
<span class="lineNum">      97 </span>                : 
<span class="lineNum">      98 </span><span class="lineCov">         102270 :             for (size_t i = 0; i &lt; aminoacids.size(); ++i)</span>
<span class="lineNum">      99 </span>                :             {
<span class="lineNum">     100 </span><span class="lineCov">         292712 :                 for (TripletsIterator triplet = GeneticCode::triplets(aminoacids[i]); !triplet.end(); ++triplet)</span>
<span class="lineNum">     101 </span>                :                 {
<span class="lineNum">     102 </span><span class="lineCov">         229262 :                     insert_into(tval.first, *triplet);</span>
<span class="lineNum">     103 </span><span class="lineCov">         229262 :                     minimize(min_dist, triplet-&gt;distance(pos_triplet, matrix));</span>
<span class="lineNum">     104 </span><span class="lineCov">          63450 :                 }</span>
<span class="lineNum">     105 </span>                :             }
<span class="lineNum">     106 </span><span class="lineCov">          38820 :             tval.second = min_dist;</span>
<span class="lineNum">     107 </span>                : 
<span class="lineNum">     108 </span><span class="lineCov">          38820 :             if (min_dist != ZERO_DISTANCE)</span>
<span class="lineNum">     109 </span>                :             {
<span class="lineNum">     110 </span><span class="lineCov">         204412 :                 for (TripletList::const_iterator itl = tval.first.begin(); itl != tval.first.end(); ++itl)</span>
<span class="lineNum">     111 </span>                :                 {
<span class="lineNum">     112 </span><span class="lineCov">         173334 :                     if ((*itl).distance(pos_triplet) == min_dist) insert_into(min_list.first, *itl);</span>
<span class="lineNum">     113 </span>                :                 }
<span class="lineNum">     114 </span>                :             }
<span class="lineNum">     115 </span><span class="lineCov">          38820 :             min_list.second = min_dist;</span>
<span class="lineNum">     116 </span>                : 
<span class="lineNum">     117 </span><span class="lineCov">          38820 :             return min_list;</span>
<span class="lineNum">     118 </span>                :         }
<span class="lineNum">     119 </span>                :     };
<span class="lineNum">     120 </span>                : 
<span class="lineNum">     121 </span>                :     /* Lista de Resistencias */
<span class="lineNum">     122 </span>                :     typedef std::list&lt;ResistancePosition&gt; Resistances;
<span class="lineNum">     123 </span>                : 
<span class="lineNum">     124 </span>                : private:
<span class="lineNum">     125 </span>                :     Resistances     resistances;
<span class="lineNum">     126 </span>                : 
<span class="lineNum">     127 </span>                : public:
<a name="128"><span class="lineNum">     128 </span>                : </a>
<span class="lineNum">     129 </span>                :     /*! Constructor del tipo antiviral con todos los parametros */
<span class="lineNum">     130 </span><span class="lineCov">             63 :     ResisBasedAntiviral(const std::string&amp; name, size_t id, AvType avtype, AvClass avclass)</span>
<span class="lineNum">     131 </span><span class="lineCov">             63 :             : Antiviral(name)</span>
<span class="lineNum">     132 </span>                :     {
<span class="lineNum">     133 </span><span class="lineCov">             63 :         set_attrib(&quot;id&quot;, id);</span>
<span class="lineNum">     134 </span><span class="lineCov">            126 :         set_attrib(&quot;class&quot;, avclass);</span>
<span class="lineNum">     135 </span><span class="lineCov">            126 :         set_attrib(&quot;Type&quot;, avtype);</span>
<span class="lineNum">     136 </span><span class="lineCov">             63 :     }</span>
<a name="137"><span class="lineNum">     137 </span>                : </a>
<span class="lineNum">     138 </span>                :     /*! Constructor por copia */
<span class="lineNum">     139 </span><span class="lineCov">             30 :     ResisBasedAntiviral(const ResisBasedAntiviral&amp; other)</span>
<span class="lineNum">     140 </span><span class="lineCov">             30 :             : Antiviral(other), resistances(other.resistances)</span>
<span class="lineNum">     141 </span><span class="lineCov">             30 :     {}</span>
<span class="lineNum">     142 </span>                : 
<span class="lineNum">     143 </span>                :     /*! Obtener la lista de resistencias */
<span class="lineNum">     144 </span>                :     inline const Resistances&amp; get_resistances() const
<span class="lineNum">     145 </span>                :     {
<span class="lineNum">     146 </span>                :         return resistances;
<span class="lineNum">     147 </span>                :     }
<span class="lineNum">     148 </span>                : 
<span class="lineNum">     149 </span>                :     /*! Agregar una resistencia en una posicion determinada. */
<span class="lineNum">     150 </span>                :     ResisBasedAntiviral&amp; add_resistance(size_t pos, const std::string&amp; aminoacid);
<span class="lineNum">     151 </span>                : 
<span class="lineNum">     152 </span>                :     /*! Agregar un nuevo atributo al antiviral.*/
<span class="lineNum">     153 </span>                :     ResisBasedAntiviral&amp; add_attribute(const std::string&amp; attrib, const std::string&amp; value);
<span class="lineNum">     154 </span>                : 
<span class="lineNum">     155 </span>                :     /*! Imprime la información del Antiviral.*/
<span class="lineNum">     156 </span>                :     void print_antiviral() const;
<span class="lineNum">     157 </span>                : 
<span class="lineNum">     158 </span>                :     /*! Imprime las resistencas. */
<span class="lineNum">     159 </span>                :     void print_resistances() const;
<span class="lineNum">     160 </span>                : 
<span class="lineNum">     161 </span>                :     /*! Combina otro antiviral con este */
<span class="lineNum">     162 </span>                :     void combine_with(ResisBasedAntiviral&amp; other) const;   
<span class="lineNum">     163 </span>                : 
<span class="lineNum">     164 </span>                :     /*! Dada una secuencia, saber si esta aplica a este antiviral */
<span class="lineNum">     165 </span>                :     virtual float applies(const NucSequence&amp; sequence) const;
<span class="lineNum">     166 </span>                : 
<span class="lineNum">     167 </span>                :     /*! Devuelve las mutantes luego de aplicar este antiviral a la secuencia */
<span class="lineNum">     168 </span>                :     virtual void mutate_sequence(const NucSequence&amp; sequence, MutantDist&amp; mutations) const;
<span class="lineNum">     169 </span>                : };
<span class="lineNum">     170 </span>                : 
<span class="lineNum">     171 </span>                : /*! Una mutante describe la secuencia y el antiviral que se aplico */
<span class="lineNum">     172 </span>                : typedef std::pair&lt;Antiviral, NucSequence&gt; Mutant;
<span class="lineNum">     173 </span>                : 
<span class="lineNum">     174 </span>                : #endif
<span class="lineNum">     175 </span>                : 
</pre>
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